However, procheck ramachandran is deprecated these days as it is based on older data than say molprobity. Obviously that won't matter just for a list of phi/psi angles, but might affect selections e.g. what it thinks are in a helix (cf Eleanor's message)
m On Wed, 2009-01-14 at 14:39 -0500, Edward A. Berry wrote: > John Pak wrote: > > Hi, sorry if this was posted earlier. How can I calculate a > > Ramachandran plot, but output the information to a text file list? > > i.e. something like Ala51, phi=X, psi=Y. > > > > I can't seem to find this information in the ccp4 SFCheck/Procheck log > > file. > > > > And lets not forget procheck, since its included with ccp4 and you > probably already have it. After you run procheck on your protein > (procheck pdbname.pdb 1.8), there is a text file pdbname.rin > which lists phi, psi, omega and sidechain dihedrals for each residue: > > > phi psi omega chi1 chi2 chi3 chi4 > 14ASN A 15 E -89.06 141.45-179.73 -63.59 -55.39 999.90 999.90 -2.14 > 0.00 34.00 89.18 88.838 88.830 8 45 1.980 0.762 > 15VAL A 16 E-139.67 138.33 177.89-170.03 999.90 999.90 999.90 0.00 > 0.00 36.23 87.91 86.643 87.253 8 50 0.147 0.499 > 16THR A 17 E-144.59 139.86-179.12 51.94 999.90 999.90 999.90 -2.64 > 0.00 34.56 84.27 86.238 85.020 8 40 0.421 0.536 > > You also have a .ps file pdbname_01.ps with the graphical ramachandran > which you can view with gv or gs, or convert to pdf with ps2pdf > > DSSP also list phi-psi angles, in two columns far to the right. > > Ed -- *********************************************************************** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455 E-mail: martyn.w...@stfc.ac.uk * * Fax: +44 1925 603825 Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***********************************************************************
